Chapter 1- An invisible world Flashcards
Microorganisms/microbes
Very small organisms that are generally too small to see without a microscope (some parasites and fungi are exceptions). All microbes, even viruses and prions, can be considered forms of life even though they aren’t organisms
Fermented foods and beverages
Includes beer, wine, bread, yogurt, cheese, and pickled vegetables. Microbial fermentation is required to produce these foods. It can preserve or enhance the flavor of food
Microbial fermentation
A process that uses bacteria, mold, or yeast to convert carbohydrates to alcohol, gases, and organic acids
How did prehistoric people attempt to treat disease?
Through the use of fungi that had medicinal properties. There is some evidence that people made incisions filled with herbs and then burned the herbs to treat disease
When was quarantine used in ancient civilizations?
People with leprosy and some other diseases were often contained, indicating that people knew some diseases could be spread to others. However, leprosy progresses slowly, so people usually transmitted the disease before they were quarantined.
Miasma hypothesis
The Greeks and Romans believed that disease was caused by “bad air”, and their hygiene practices were based on this idea. The idea was that if the smell was sewage was present and people got sick, it was from the smell rather than contamination from the sewage. Also, lack of hygiene made people smell and this was thought to make people sick (due to the smell). The Romans built complex sanitation infrastructure, including aqueducts and sewers (including the Cloaca Maxima), also based on the miasma hypothesis. This may have protected them from waterborne illnesses
What did Hippocrates believe caused disease?
At the time, many people believed that disease was caused by supernatural forces. However, Hippocrates believed that diseases had natural causes from the patient’s body or the environment. Hippocrates wrote medical textbooks (the Hippocratus Corpus) and the Hippocratic Oath.
Thucydides
Greek philosopher- he advocated for evidence-based analysis of cause and effect reasoning. He demonstrated an early understanding of immunity by observing that survivors of the plague did not get re-infected.
Marcus Terentius Varro
Roman writer, was one of the first people to suggest that things we couldn’t see (microorganisms) could cause disease
Antonie van Leeuwenhoek
The first person to develop a lens powerful enough to view microbes in 1675. He was able to observe single celled organisms. He called them animalcules, although they were actually bacteria and protists.
Golden Age of microbiology
The time between 1857 and 1914, where there were many new discoveries in microbiology. This includes the findings of Louis Pasteur and Robert Koch
Louis Pasteur
Showed that individual microbial strains had unique properties. He also found that fermentation is caused by microorganisms. He invented pasteurization and developed vaccines to treat disease in animals and humans, including a vaccine for rabies
Pasteurization
A process used to kill microorganisms responsible for spoilage
Robert Koch
Demonstrated the connection between an isolated microbe and disease in humans. He discovered the bacteria that caused anthrax, cholera, and tuberculosis.
Microscopes
Produce magnified images of microorganisms, human cells and tissues, and many other types of specimens too small to be observed with the naked eye
Stains and dyes
Used to add color to microbes so they can be better observed under a microscope. Some dyes can be used on living microbes, while others require that the specimens be fixed with chemicals or heat before staining. Some stains only work on certain types of microbes because of differences in their cellular chemical composition.
Growth media
Used to grow microorganisms in a lab setting. Some media are liquids; others are more solid or gel-like. A growth medium provides nutrients, including water, various salts, a source of carbon (like glucose), and a source of nitrogen and amino acids (like yeast extract) so microorganisms can grow
and reproduce. Ingredients in a growth medium can be modified to grow unique types of microorganisms.
Petri dish
Flat-lidded dish that is typically 10–11 cm in diameter and 1–1.5 cm high. Petri dishes made out of either plastic or glass are used to hold growth media
Purpose of test tubes
Used to grow microbes in broth or solid/semi solid growth media
Microincinerators
Used for the same purpose as a Bunsen burner. They are generally replacing microincinerators because they don’t have the risk of an open flame
Inoculation loop
A tool that ends in a small wire loop. The loop can be used to streak microorganisms on agar in a Petri dish or to transfer them from one test tube to another. Before each use, the inoculation loop must be sterilized so cultures do not become contaminated.
Taxonomy
The classification, description, identification, and naming of living organisms
Classification
The practice of organizing organisms into different groups based on their shared characteristics
Carolus Linnaeus
Swedish zoologist and physician. He published Systema Naturae in 1735, which proposed the Linnaean taxonomy. This was a system of categorizing and naming organisms that scientists could use to name organisms with standardized terminology.
Linnaean taxonomy
Divided the natural world into animal, plant, and mineral kingdoms. Plant and animal organisms were grouped using a hierarchy of levels and sublevels based on their characteristics. The mineral kingdom was later removed
Levels in Linnaean taxonomy (6)
Kingdom, class, order, family, genus, species. Species is the most specific unit
Phylogenies
Evolutionary relationships between different species. Phylogenetic trees were used to depict these relationships. Modern phylogenic analyses include genetic, biochemical, and embryological comparisons
How did Linnaeus’ phylogenetic tree change over time?
His original tree contained 2 branches- plants and animals. Eventually, the kingdoms Protista were added for unicellular organisms, Monera for unicellular organisms whose cells lack nuclei (bacteria), and fungi. A superkingdom level was added to distinguish between eukaryotes and prokaryotes
Empire Prokaryota vs Empire Eukaryota
Distinguishes between organisms that have membrane bound nuclei and those that don’t. Prokaryotes only include the kingdom Monera, while eukaryotes include fungi, Protista, Plantae, and Animalia
Why aren’t viruses depicted in phylogenetic trees?
They aren’t made up of cells, so they don’t fit in any kingdoms
Why was the development of molecular genetics important to phylogeny?
It allowed for a standardized way to compare all living organisms without relying on observable characteristics, which can be subjective. Organisms are considered to be related if they have more similar nucleic acids and proteins
Carl Woese
In the 1970s, he created a phylogenetic tree based on gene sequences that coded for small subunit rRNA in different organisms. He discovered a type of bacteria called archaea was significantly different from other bacteria and eukaryotes based on its rRNA sequence. As a result, 3 domains were added above kingdoms- archaea, bacteria, and eukarya. These 3 domains evolved from a common ancestral cell type
Horizontal gene transfer
When a gene of one species is absorbed into another organism’s genome. This is common in microorganisms, which can make it difficult to determine how organisms are evolutionarily related
Binomial nomenclature
A naming system used to identify organisms- uses genus and a specific epithet (like sapien in homo sapiens, homo is the genus). Names can reflect a specific characteristic of the organism or the name of the scientist who discovered them. Usually, a name will be shortened to the first initial of the genus followed by the epithet. The name of each species is unique and standardized among scientists.
Bergey’s manuals
Standard references for identifying and classifying different prokaryotes. Many bacteria look identical, so they are differentiated based on DNA and rRNA sequencing or serological tests that identify antibodies reacting against proteins produced by the species
How big does an object have to be to be visible without a microscope?
100 micrometers. Most microorganisms are much smaller than this. Bacteria cells are 1 micrometer and viruses are 10 times smaller than bacteria.
Acellular
Not composed of cells. Viruses are acellular microorganisms. Microorganisms can also be unicellular or multicellular
Which domains are microorganisms found in?
All 3 domains- archaea, bacteria, and eukarya. Viruses do not fall in any of these domains. The domains bacteria and archaea are prokaryotic, while eukarya contains eukaryotic organisms.
Pathogens
Microorganisms that cause disease in humans and other animals
Are bacteria considered prokaryotic or eukaryotic?
Prokaryotic- their DNA is not located within a true nucleus
Peptidoglycan
The molecule that is located in the cell walls of most bacteria
Bacteria are usually described in terms of
Shape
Shapes of bacteria (3)
- Spherical (coccus)
- Rod-shaped (bacillus)
- Curved (spirillum, spirochete, or vibrio)
Metabolic capabilities of bacteria
They have a wide range of metabolic capabilities and can grow in many different environments. Oxygenic cyanobacteria is an example of a photosynthetic bacteria- it derives energy from sunlight and carbon dioxide. Other types of bacteria do not use photosynthesis- they use organic or inorganic compounds to obtain energy
Archaea
Unicellular prokaryotic organisms. Unlike bacteria, archaeal cell walls contain pseudopeptidoglycan rather than peptidoglycan. Like bacteria, they are found in almost every habitat, even extreme environments. They don’t seem to be pathogenic to humans.
Which organisms does domain Eukarya contain?
All eukaryotes, including those that are unicellular or multicellular. This includes protists, fungi, plants, and animals. Eukaryotic cells contain a nucleus.
Protists
An informal grouping of eukaryotes that aren’t plants, animals, or fungi. Algae and protozoa are examples
Algae
Eukaryotic protists that can be unicellular or multicellular and have different sizes, appearances, and habitats. They can reproduce sexually or asexually. Their cell walls are made of cellulose (a carbohydrate). They are photosynthetic, obtaining energy from the sun and releasing oxygen and carbohydrates into the environment.
Uses of algae
Many products contain carrageenan or alginic acid, which is derived from algae. This includes some brands of ice cream, beverages, lipstick, and toothpaste. Agar is a gel derived from algae and used to grow microorganisms in Petri dishes. Algae can also be used to produce biofuels.
Protozoa
Mainly chemoheterotrophic protists that provide nutrients for other organisms- act as a backbone of ecosystems. They move using cilia or flagella. Some are pseudopods- they extend part of their membrane to move around. They can be photosynthetic or feed on organic material, and some are parasitic while some survive on their own. Some protozoa are pathogenic- malaria, giardiasis, amoebic dysentery
Fungi
Eukaryotes. Some multicellular fungi (mushrooms) resemble plants, but they have different properties- they are not photosynthetic and their cell walls are usually made of chitin instead of cellulose. Live in dry conditions, are plant decomposers, and around 100 species are human pathogens. Unicellular fungi (yeasts) are found in many different environments. They can be pathogenic, but are also used to cause bread to rise and to ferment beverages
Molds
Multicellular fungi that contain masses of mycelia which are made up of long filaments (hyphae) that form visible colonies. They play a role in decomposing dead plants and animals. They can cause allergies, and some produce disease causing metabolites (mycotoxins). They are used to make certain drugs, like penicillin
Types of fungi (3)
- Multicellular- mushrooms
- Yeasts (unicellular)
- Molds
Types of protists (2)
- Algae
- Protozoa
Helminths
Multicellular eukaryotic parasitic worms- diseases caused by helminths involve microscopic eggs and larvae. Hooks that attach to the intestines- exposure occurs through eating pork or beef that isn’t adequately cooked- use a person’s nutrients once attached to the intestines. An example is guinea worm disease
Viruses
Acellular microorganisms- they are made of proteins and genetic material (DNA or RNA). They are inert outside of a host organism, but once they are inside a host cell, they use the cell’s machinery to multiply and infect other hosts. They can infect human cells or the cells of other microorganisms. Not all viruses are pathogenic. Considered obligate intracellular parasites
Microbiology
Encompasses the study of all different types of microorganisms- bacteriology, mycology (fungi), protozoology (protozoa), parasitology, virology, and immunology
Why is immunology included in microbiology?
Host-pathogen interactions are crucial to our understanding of infectious disease processes
How have microbes shaped our energy cycles and the atmosphere?
Microbes are thought to be anaerobic originally, then evolved to be photosynthetic and released oxygen. This caused the environment to be oxygenated, and some microorganisms became aerobic. Early microbes eventually evolved into multicellular plants and animals, including humans. They play a crucial role in all ecosystems- fix nitrogen for plants to use, they are the, basis of the food chain in oceans, rivers, and lakes (organisms feed on them), responsible for the cycling of minerals
6 rules to be fulfilled by a living organism
- Metabolism
- Reproduction
- Differentiation
- Communication
- Movement
- Evolution
What does metabolism mean in regard to cells?
The cell is an open system- it can take in chemicals from the environment, transform them, and release new chemicals into the environment. Compounds are broken down to produce energy or other compounds
What does reproduction mean in regard to cells?
Chemicals from the environment are turned into new cells under the direction of preexisting cells. The cell needs to reproduce by itself, even if it’s inside another organism
How is yeast an example of fermentation?
Yeast is a microorganism responsible for making bread rise. Yeast cells metabolize the carbohydrates in flour and produce carbon dioxide, which causes the bread to rise.
Microbiota
Microbes normally present in and on the human body are called microbiota (like a microbiome)- found in the gut, skin, hair, etc, and in the organs of other plants and animals. Microbiota prevents growth of pathogens and produce growth factors, like folic acid and vitamin K (produced by bacteria only). If you are exposed to pathogens, they transiently become part of your microbiota. If there is an imbalance, like if you cut your skin, the pathogens can enter your body and cause disease
Which rRNA do we use to classify bacteria and eukaryotic cells?
For bacteria, we use 16s rRNA. We use 18s rRNA for eukaryotic organisms
Prokaryotes
Lack a nuclear membrane and include bacteria and archaea
Eukaryotes
Possess a nuclear membrane (nucleus), include fungi, protozoa, and algae
How do bacteria reproduce?
Binary fission
How do bacteria make ATP?
Different types of bacteria make ATP using different sources. Some can even switch between the different types of sources they use. Some need oxygen, others will die in the presence of oxygen. Some need less oxygen than the amount they get from atmospheric oxygen.
Endospores
Bacterial spores that are located inside of the cell (where the endo comes from)
Coccus
Spherical bacteria
Bacillus
Rod shaped
Vibrio
Curved rod
Coccobacillus
An elongated sphere (sort of ellipse shaped)
Spirillum
Wave shaped
Spirochete
Corkscrew shaped
Archaea are divided into (3)
- Methanogens
- Extreme halophiles
- Extreme thermophiles
Mycoses
Humid places on the body, like the armpits or between toes, are typical locations for fungal infections. Opportunistic pathogens- usually located in us, but don’t cause disease unless given an opportunity (like with immunosuppression). Examples include candida, ringworm, athlete’s foot, jock itch, etc
Prions
Not cells but proteins in a malformed conformation- can induce other proteins in the same family to be malformed and cause plaques. Acellular, obligate intracellular “parasites”. Examples- Creutzfeldt-Jakob Disease, Fatal Familial Insomnia, Mad cow disease
Uses of microbes in our lives (6)
- We use them to synthesize minerals- some vitamins are produced by bacteria
- Use them to make certain foods
- Used as digestive aids (probiotics are microorganisms)
- Produce acetone- used for nail polish remover
- Used to synthesize insulin
- Vaccines are produced by bacteria
Resistance
The ability of the body to ward off disease. Resistance factors include skin, stomach acid, and antimicrobial chemicals
Biofilms
Microbes attach to solid surfaces and grow into masses. When bacteria grow on our body or in our body, they usually grow as biofilms (bacteria do not live as individual cells in most cases). They will grow on rocks, pipes, teeth, and medical implants
